I just purchased a used MIM strat. The guy I bought it from didn't have a tremolo cover for it and said that he had tried to fit it with ebay trem covers but the screw holes didn't line up. Has anyone experienced this and does anyone know why this may be the case and how to remedy it? I'm also curious about the model. When I took the pickguard off, it had R markings in a few places inside. Does anyone know what the R stands for and could it have anything to do with the trem cover not fitting? The strat is a 2000 according to markings inside. I've not taken the neck off to check, but the serial number is consistent with the date inside the body, so I doubt that the body is not original but a fake neck is easier to spot than a fake body.

When you say "trem cover" do you mean the chrome cover that goes over the saddles and trem plate, or the rear cover that enclosed the spring cavity?????
I think you mean the tremolo cavity cover. For a MIM Strat, they should be very easy to find. Some people actually think that a Strat sounds better with it off. It is not a vintage guitar, so I would obtain a cover, re-drill holes as necessary, and install it, or not, up to you.
Go to Fenders website(which you are on) and compare specs from recent models, and see what your guitar matches.

You could also open up the holes to look like slots to make it fit or buy a slotted aftermarket plate.

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